Description Usage Arguments Details Value Author(s) See Also
View source: R/exportFunctions.R
This function exports a network in edge and node list files in a format suitable for importing to Cytoscape.
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adjMat |
adjacency matrix giving connection strengths among the nodes in the network. |
edgeFile |
file name of the file to contain the edge information. |
nodeFile |
file name of the file to contain the node information. |
weighted |
logical: should the exported network be weighted? |
threshold |
adjacency threshold for including edges in the output. |
nodeNames |
names of the nodes. If not given, |
altNodeNames |
optional alternate names for the nodes, for example gene names if nodes are labeled by probe IDs. |
nodeAttr |
optional node attribute, for example module color. Can be a vector or a data frame. |
includeColNames |
logical: should column names be included in the output files? Note that Cytoscape can read files both with and without column names. |
If the corresponding file names are supplied, the edge and node data is written to the appropriate files. The edge and node data is also returned as return value (see below).
A list with the following componens:
egdeData |
a data frame containing the edge data, with one row per edge |
nodeData |
a data frame containing the node data, with one row per node |
Peter Langfelder
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